Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015921.1 Corchorus capsularis cultivar CVL-1 contig15942, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 127491
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:4463 original size:9 final size:9
Alignment explanation
Indices: 4449--4485 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
4439 TATTATCAAT
4449 ATGAAGATG
1 ATGAAGATG
*
4458 AGGAAGATG
1 ATGAAGATG
4467 ATGAAGATG
1 ATGAAGATG
4476 ATGAAGATG
1 ATGAAGATG
4485 A
1 A
4486 AGTCTATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (9 bp):
ATGAAGATG
Found at i:5884 original size:16 final size:16
Alignment explanation
Indices: 5863--5899 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5853 AAGTCAACGT
*
5863 CCCGAACACACCCGAA
1 CCCGAAAACACCCGAA
*
5879 CCCGAAAATACCCGAA
1 CCCGAAAACACCCGAA
5895 CCCGA
1 CCCGA
5900 CCCGAGCCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.46, G:0.14, T:0.03
Consensus pattern (16 bp):
CCCGAAAACACCCGAA
Found at i:6670 original size:11 final size:11
Alignment explanation
Indices: 6654--6695 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
6644 TATCGAAAGT
6654 GAACCCGATCC
1 GAACCCGATCC
*
6665 GAACCCGAACCC
1 GAACCCG-ATCC
6677 GAACCCGATCC
1 GAACCCGATCC
*
6688 GAGCCCGA
1 GAACCCGA
6696 ACCCGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.29, C:0.45, G:0.21, T:0.05
Consensus pattern (11 bp):
GAACCCGATCC
Found at i:6673 original size:23 final size:23
Alignment explanation
Indices: 6654--6702 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6644 TATCGAAAGT
*
6654 GAACCCGATCCGAACCCGAACCC
1 GAACCCGATCCGAACCCGAAACC
* *
6677 GAACCCGATCCGAGCCCGAACCC
1 GAACCCGATCCGAACCCGAAACC
6700 GAA
1 GAA
6703 AATACCTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.45, G:0.20, T:0.04
Consensus pattern (23 bp):
GAACCCGATCCGAACCCGAAACC
Found at i:6674 original size:6 final size:6
Alignment explanation
Indices: 6654--6702 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
6644 TATCGAAAGT
* * *
6654 GAACCC G-ATCC GAACCC GAACCC GAACCC G-ATCC GAGCCC GAACCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
6700 GAA
1 GAA
6703 AATACCTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 8 0.23
6 27 0.77
ACGTcount: A:0.31, C:0.45, G:0.20, T:0.04
Consensus pattern (6 bp):
GAACCC
Found at i:6674 original size:17 final size:17
Alignment explanation
Indices: 6669--6701 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6659 CGATCCGAAC
6669 CCGAACCCGAACCCGAT
1 CCGAACCCGAACCCGAT
*
6686 CCGAGCCCGAACCCGA
1 CCGAACCCGAACCCGA
6702 AAATACCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.48, G:0.21, T:0.03
Consensus pattern (17 bp):
CCGAACCCGAACCCGAT
Found at i:6715 original size:16 final size:16
Alignment explanation
Indices: 6694--6755 Score: 90
Period size: 16 Copynumber: 3.9 Consensus size: 16
6684 ATCCGAGCCC
6694 GAACCCGAAAATACCT
1 GAACCCGAAAATACCT
* *
6710 GAACCCAAAAATACCC
1 GAACCCGAAAATACCT
*
6726 GAACCCGAAAATATCT
1 GAACCCGAAAATACCT
6742 GAACCCG-AAATACC
1 GAACCCGAAAATACC
6756 CAAACCCAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
15 6 0.15
16 34 0.85
ACGTcount: A:0.45, C:0.32, G:0.11, T:0.11
Consensus pattern (16 bp):
GAACCCGAAAATACCT
Found at i:6756 original size:31 final size:32
Alignment explanation
Indices: 6691--6762 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
6681 CCGATCCGAG
6691 CCCGAACCCGAAAATACCTGAACCCAAAAATA
1 CCCGAACCCGAAAATACCTGAACCCAAAAATA
* *
6723 CCCGAACCCGAAAATATCTGAACCC-GAAATA
1 CCCGAACCCGAAAATACCTGAACCCAAAAATA
*
6754 CCCAAACCC
1 CCCGAACCC
6763 AAGCCCGCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 13 0.35
32 24 0.65
ACGTcount: A:0.43, C:0.38, G:0.10, T:0.10
Consensus pattern (32 bp):
CCCGAACCCGAAAATACCTGAACCCAAAAATA
Found at i:18002 original size:22 final size:22
Alignment explanation
Indices: 17970--18012 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17960 AAAATCCTAA
17970 AACAGAGTTCCT-TTAACCCATC
1 AACAGAGTTCCTATT-ACCCATC
*
17992 AACAGATTTCCTATTACCCAT
1 AACAGAGTTCCTATTACCCAT
18013 AAAACCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
AACAGAGTTCCTATTACCCATC
Found at i:22021 original size:40 final size:40
Alignment explanation
Indices: 21966--22048 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
21956 CAAACCATCC
21966 AAGGAGGAGTGTTAGATTTGAATGTGCTTGCTAGCTGTTT
1 AAGGAGGAGTGTTAGATTTGAATGTGCTTGCTAGCTGTTT
*
22006 AAGGAGGAGTGTTAGATTTGAATGTGTTTGCTAGCTGTTT
1 AAGGAGGAGTGTTAGATTTGAATGTGCTTGCTAGCTGTTT
22046 AAG
1 AAG
22049 TTAATGGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.06, G:0.33, T:0.37
Consensus pattern (40 bp):
AAGGAGGAGTGTTAGATTTGAATGTGCTTGCTAGCTGTTT
Found at i:24914 original size:426 final size:430
Alignment explanation
Indices: 24201--25210 Score: 1205
Period size: 426 Copynumber: 2.3 Consensus size: 430
24191 TAACGCGTTA
* * * **
24201 GCTTTTATTTTAATT-TTT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAATAGACA
1 GCTTTT-TTTT-ATTCTTTGTTCTATTTGTCAG-TTAAGGTGATTCATGTGTCTATTAAAAGGTA
* * * * *
24264 ATTTCATGATCTACAATTTTCATGAAGAACCCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAA
63 ATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAA
** * * * * * *
24329 TGCTTCCGAAATTTTGTGGTTTTGATTGCCGGTCAATTTAATATCATATAATTTTTTGTCCACAT
128 TGCTTTTGAAATTTGGTCGTTTCGATTGCCGATCAATTTAATACCATATAATTTTTCGTCCACAT
* * * * *
24394 GTCCGATTGAAATTATTGAAGTGTCAATTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGG
193 ATCCGATTGAAATTATTCAAGTGTCAATTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGA
* *
24459 ACCCGAAAACTAAATTTGATCTACGAGTTTCATGGAGGGTTCAAAAGGGAATTTTTATGCTTCAA
258 ACCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTAATGCTTCAA
* ** * *
24524 GATCTCCATTAACAAACA-TTCTTATTTGGATTATTTATCAAATGACCCTCATATTTTTCTACTT
323 GATATCCATTAACAAACATTTCTTATTTAAATTAGTTATCAAATGACCCTCATACTTTTCTA-TT
* *
24588 TT-TACTACTTAGTCCTTTAC-AA-ATTCTATCTTA-ATCTAAC
387 TTATACTACTTAGTCATTAACAAATATTCTATCTTATATCTAAC
*
24628 G-TTTTTTTTATTCTTTGTTCTATTTGTCTAGTTAAGTTGATTCATGTGTCTATTAAAAGGTAAT
1 GCTTTTTTTTATTCTTTGTTCTATTTGTC-AGTTAAGGTGATTCATGTGTCTATTAAAAGGTAAT
* * * * *
24692 TTCATGATCTAGAGCTTTCATGAAGGGCTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAAAAT
65 TTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTC-TAAAAAAT
* ** *
24757 GCTTTTTAAATTTGGTCGTTTCGATTGTTGATCTATTTAATACCATATAA-TTTTCGATCCACAT
129 GCTTTTGAAATTTGGTCGTTTCGATTGCCGATCAATTTAATACCATATAATTTTTCG-TCCACAT
** *
24821 ATCCGATT-AAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGAAG
193 ATCCGATTGAAA-TTATTCAAGTGTCAATTAAAAGGTTACTGCATGATCTACGACTTTCATGAAG
* * * *
24885 AACCCG-AGAGTTAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTAATGTTTCA
257 AACCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTAATGCTTCA
* *
24949 AGATATCCATTAAGAAATATTTTCTTATTTAAATTAGTTATCAAATGACCCTCATACTTTTCTAT
322 AGATATCCATTAACAAACA-TTTCTTATTTAAATTAGTTATCAAATGACCCTCATACTTTTCTAT
*
25014 TTTATACTACTTAGTCATTAACAAATTATTCTATCTTATTCGATTTAAC
386 TTTATACTACTTAGTCATTAACAAA-TATTCTATCTTA-T--ATCTAAC
* *
25063 GCTTCATTTTTTTTATTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCATGTGTCTATTAAAA
1 G---C-TTTTTTTTA--TTCTTTGTTCTATTTGT-CAGTTAAGGTGATTCATGTGTCTATTAAAA
* * * ** * *
25128 GGTAATTTTATGATCTACAACTTTCATGAAAGACTAAAAAGTTAATTTTCATGTTTCAATTCTAA
59 GGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAA
*
25193 AAAATACTTTTGAAATTT
124 AAAATGCTTTTGAAATTT
25211 TGTGAATTCG
Statistics
Matches: 491, Mismatches: 68, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
424 3 0.01
425 7 0.01
426 166 0.34
427 117 0.24
428 55 0.11
429 2 0.00
431 11 0.02
435 7 0.01
440 9 0.02
441 18 0.04
442 95 0.19
443 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (430 bp):
GCTTTTTTTTATTCTTTGTTCTATTTGTCAGTTAAGGTGATTCATGTGTCTATTAAAAGGTAATT
TCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAATGC
TTTTGAAATTTGGTCGTTTCGATTGCCGATCAATTTAATACCATATAATTTTTCGTCCACATATC
CGATTGAAATTATTCAAGTGTCAATTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACC
CGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTAATGCTTCAAGAT
ATCCATTAACAAACATTTCTTATTTAAATTAGTTATCAAATGACCCTCATACTTTTCTATTTTAT
ACTACTTAGTCATTAACAAATATTCTATCTTATATCTAAC
Found at i:25660 original size:23 final size:23
Alignment explanation
Indices: 25630--25732 Score: 163
Period size: 23 Copynumber: 4.5 Consensus size: 23
25620 TGCTTGGCTC
*
25630 CCGACCACTTCCAAGCCTAGCGA
1 CCGACCACTTACAAGCCTAGCGA
*
25653 CCGACCACTTACAAGTCTAGCGA
1 CCGACCACTTACAAGCCTAGCGA
25676 CCGACCACTTACAAGCCTAGCGA
1 CCGACCACTTACAAGCCTAGCGA
*
25699 CCGACCACTTACAAGCCT-GCCGC
1 CCGACCACTTACAAGCCTAG-CGA
25722 CCGACCACTTA
1 CCGACCACTTA
25733 TGACCACAAG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
22 1 0.01
23 74 0.99
ACGTcount: A:0.27, C:0.42, G:0.17, T:0.15
Consensus pattern (23 bp):
CCGACCACTTACAAGCCTAGCGA
Found at i:25808 original size:26 final size:26
Alignment explanation
Indices: 25772--25893 Score: 149
Period size: 26 Copynumber: 4.7 Consensus size: 26
25762 GCCAGCTGGC
* *
25772 ACTCCACACGTGAGCTCCAATGTACG
1 ACTCCACACGTGACCTCCAACGTACG
25798 ACTCCACACGTGACCTCCAACGTACG
1 ACTCCACACGTGACCTCCAACGTACG
* *
25824 ACTCCTCACGTGACCTCCAACGGAC-
1 ACTCCACACGTGACCTCCAACGTACG
* *
25849 ACCTTCAACACGTGACCTCCGAA-GTACA
1 A-C-TCCACACGTGACCTCC-AACGTACG
25877 ACTCCACACGTGACCTC
1 ACTCCACACGTGACCTC
25894 GCGCGTGTGA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.01
26 62 0.74
27 18 0.21
28 3 0.04
ACGTcount: A:0.27, C:0.40, G:0.16, T:0.17
Consensus pattern (26 bp):
ACTCCACACGTGACCTCCAACGTACG
Found at i:27082 original size:42 final size:41
Alignment explanation
Indices: 27021--27141 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 41
27011 CAGCCCTTGT
*
27021 CGAACGACAGCCCCCCAGAACAACCAGAAGTGACGAAAGTGC
1 CGAACGACAG-CTCCCAGAACAACCAGAAGTGACGAAAGTGC
* * * *
27063 CGAACGACAGCTTCTCAGAACAACCGGAAGTGATGAAAGTGT
1 CGAACGACAGC-TCCCAGAACAACCAGAAGTGACGAAAGTGC
*
27105 CGAACGACAGCTCCCTAGAACAACCAAAAGTGACGAA
1 CGAACGACAGCTCCC-AGAACAACCAGAAGTGACGAA
27142 CGCCTCCGAG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.06
42 64 0.94
ACGTcount: A:0.39, C:0.28, G:0.23, T:0.10
Consensus pattern (41 bp):
CGAACGACAGCTCCCAGAACAACCAGAAGTGACGAAAGTGC
Found at i:27709 original size:90 final size:90
Alignment explanation
Indices: 27556--27727 Score: 290
Period size: 90 Copynumber: 1.9 Consensus size: 90
27546 AAATTATACT
* * **
27556 TGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGGGGCGATCGACAAGATTTTACCTTGACC
1 TGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACCTTGACC
27621 TAGCATGGCCCCCAACTTTTGGGAA
66 TAGCATGGCCCCCAACTTTTGGGAA
* *
27646 TGACGAACGCCCTCAATGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACCTTGACC
1 TGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACCTTGACC
27711 TAGCATGGCCCCCAACT
66 TAGCATGGCCCCCAACT
27728 GACAGGAGAT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.26, C:0.33, G:0.27, T:0.15
Consensus pattern (90 bp):
TGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACCTTGACC
TAGCATGGCCCCCAACTTTTGGGAA
Found at i:27864 original size:125 final size:126
Alignment explanation
Indices: 27640--27871 Score: 342
Period size: 125 Copynumber: 1.8 Consensus size: 126
27630 CCCCAACTTT
* * *
27640 TGGGAATGACGAACGCCCTCAATGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACC
1 TGGGAACGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACC
*
27705 TTGACCTAGCATGGCCCCCAACTGACAGGAGATTGG-AAGAAAACCATCTCTGGACAAGTA
66 TTGACCTAACATGGCCCCCAACTGACAGGAGATTGGCAAGAAAACCATCTCTGGACAAGTA
* * * *
27765 TGGGAACGATGAACGCCCCCTAGGGGCTCAACGCCAGGAGGCTAGGCGATCGACAAGAATCGACC
1 TGGGAACGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACC
* * *
27830 TTGACCTAACATGGCCCCCGA-TCGGCAGGCGATTGGCAAGAA
66 TTGACCTAACATGGCCCCCAACT-GACAGGAGATTGGCAAGAA
27872 CCATCCCTGA
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
124 1 0.01
125 88 0.94
126 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.29, T:0.14
Consensus pattern (126 bp):
TGGGAACGACGAACGCCCCCAAGGGGCTCAACGCCAGCAGGCGAGGCGATCGACAAGAATCGACC
TTGACCTAACATGGCCCCCAACTGACAGGAGATTGGCAAGAAAACCATCTCTGGACAAGTA
Found at i:28401 original size:21 final size:21
Alignment explanation
Indices: 28287--28407 Score: 66
Period size: 21 Copynumber: 5.6 Consensus size: 21
28277 GACTACCCAA
* *
28287 AAAGAGGAATGCTCTCTAAAG
1 AAAGAAGAATGCTCTCCAAAG
* * *
28308 AAAGAAAAATGCTC-CCTATG
1 AAAGAAGAATGCTCTCCAAAG
* * *
28328 -AAGAGGATTATGCACTCCAATG
1 AAAGAAGA--ATGCTCTCCAAAG
* * * *
28350 AAGGGAGAATACTCACTCCCCAAG
1 AAAGAAGAATGCT--CT-CCAAAG
28374 AAGAGAAGAATGCTCTCCAAAG
1 AA-AGAAGAATGCTCTCCAAAG
28396 AAAGAAGAATGC
1 AAAGAAGAATGC
28408 GCCCTACGAG
Statistics
Matches: 72, Mismatches: 20, Indels: 16
0.67 0.19 0.15
Matches are distributed among these distances:
19 5 0.07
20 3 0.04
21 30 0.42
22 12 0.17
23 8 0.11
24 6 0.08
25 8 0.11
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (21 bp):
AAAGAAGAATGCTCTCCAAAG
Found at i:29156 original size:58 final size:57
Alignment explanation
Indices: 28918--29265 Score: 421
Period size: 57 Copynumber: 6.1 Consensus size: 57
28908 CACCAAAGTC
* * *
28918 GAAGAAAGGAGAAATGCGTCGAACGACCAAAATCACGTTCATGCCGAAATGG-TCAAA
1 GAAGAAAGGAAAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTC-AA
* * * *
28975 GAAGAAATGAGAAATGCGTCGAATGACCAAAATCACATTCATGCCGAAATGGTTCAA
1 GAAGAAAGGAAAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTCAA
* * * * * *
29032 GAAGCAAGGAAAAATGGGTCAAACGACCACAATCACATTCAAGCC-AAGATGATTCAA
1 GAAGAAAGGAAAAATGTGTCGAACGACCAAAATCACATTCATGCCGAA-ATGGTTCAA
* * *
29089 GAAGCAAGGAAAAATGTGTCGAACGACCAAAAATTACATTCATGTCGAAATGGTTCAA
1 GAAGAAAGGAAAAATGTGTCGAACGACC-AAAATCACATTCATGCCGAAATGGTTCAA
* * *
29147 GAAGCAAGGAATAATGTGTCGAACGACCAAAAATCACATTCATGCCGAAATGGTTAAA
1 GAAGAAAGGAAAAATGTGTCGAACGACC-AAAATCACATTCATGCCGAAATGGTTCAA
* * * * *
29205 GAAGAAAGAAAAAATTGTGTCGAACGACCAAAATCAAATTTATGCCAAAATGGTTAAA
1 GAAGAAAGGAAAAA-TGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTCAA
29263 GAA
1 GAA
29266 AAAAAGTAAC
Statistics
Matches: 257, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
56 2 0.01
57 122 0.47
58 117 0.46
59 16 0.06
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.18
Consensus pattern (57 bp):
GAAGAAAGGAAAAATGTGTCGAACGACCAAAATCACATTCATGCCGAAATGGTTCAA
Found at i:29329 original size:44 final size:44
Alignment explanation
Indices: 29261--29682 Score: 666
Period size: 44 Copynumber: 9.6 Consensus size: 44
29251 AAAATGGTTA
*
29261 AAGAAAAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
* * * *
29305 ACGAAGAAAAGTAACTAGTTGATCGACCACATAACATTTAAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
* *
29349 AAGAAGAAAGGTAACTAGTCGATCGACCACATCATATTCAAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
*
29393 ACGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
* *
29437 ATGAAGAAAAGTAACTAGTCGATCGACCACATCACAATCAAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
29481 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
* ** *
29525 AAGAAGAAAAG-AACCAGTCGATCGACCACATTTCATTCGAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
29568 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
* * *
29612 AAGAAGAAAAGTAACCAGTTGAACGACCACATCACATTCAAACC
1 AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
* *
29656 AAGAAGAAATGTAACTAGTCGACCGAC
1 AAGAAGAAAAGTAACTAGTCGATCGAC
29683 ACCTAAGTAA
Statistics
Matches: 344, Mismatches: 33, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
43 39 0.11
44 305 0.89
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.16
Consensus pattern (44 bp):
AAGAAGAAAAGTAACTAGTCGATCGACCACATCACATTCAAACC
Found at i:29912 original size:58 final size:58
Alignment explanation
Indices: 29832--30010 Score: 304
Period size: 58 Copynumber: 3.1 Consensus size: 58
29822 ATCGTGGCAT
29832 ACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCAAAAGTGGCGTGCG
1 ACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCAAAAGTGGCGTGCG
* *
29890 ACAACATAGAAAGGGAAGAAGACAAGTCAAAAATTCTCAATTGCAAAAGTTGCGTGCG
1 ACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCAAAAGTGGCGTGCG
* * *
29948 ACAACATAGAAAGGGAAGAAGACAAGTAAAAAAAATCCCAATTACAAAAGTGGCGTGCG
1 ACAACATAGAAAGGGAAGAAGACAAGT-AAAAAATTCTCAATTGCAAAAGTGGCGTGCG
30007 ACAA
1 ACAA
30011 GAAAAACAAA
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 83 0.73
59 30 0.27
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (58 bp):
ACAACATAGAAAGGGAAGAAGACAAGTAAAAAATTCTCAATTGCAAAAGTGGCGTGCG
Found at i:31188 original size:45 final size:45
Alignment explanation
Indices: 31124--31236 Score: 194
Period size: 45 Copynumber: 2.6 Consensus size: 45
31114 AACCCACCCG
*
31124 ACAAATCAAAGACTCTCGGTCAAAATGTGGCGTACGACAAGTTCA
1 ACAAATCAAAGACTCTCGGTCAAAATGTGACGTACGACAAGTTCA
31169 ACAAATCAAAGACTCTCGGTCAAAATGTGACGTACGACAAGTTCA
1 ACAAATCAAAGACTCTCGGTCAAAATGTGACGTACGACAAGTTCA
*
31214 ATAAATCAAAGA-T-TCGGTCAAAA
1 ACAAATCAAAGACTCTCGGTCAAAA
31237 AAGGGCACGC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
43 10 0.15
44 1 0.02
45 55 0.83
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (45 bp):
ACAAATCAAAGACTCTCGGTCAAAATGTGACGTACGACAAGTTCA
Found at i:31250 original size:43 final size:44
Alignment explanation
Indices: 31124--31252 Score: 149
Period size: 45 Copynumber: 2.9 Consensus size: 44
31114 AACCCACCCG
*
31124 ACAAATCAAAGACTCTCGGTCAAAATGTGG-CGTACGACAAGTTCA
1 ACAAATCAAAGACTCTCGGTCAAAAAG-GGACG-ACGACAAGTTCA
* *
31169 ACAAATCAAAGACTCTCGGTCAAAATGTGACGTACGACAAGTTCA
1 ACAAATCAAAGACTCTCGGTCAAAAAGGGACG-ACGACAAGTTCA
*
31214 ATAAATCAAAGA-T-TCGGTCAAAAAAGGGCACG-CGACAAG
1 ACAAATCAAAGACTCTCGGTC-AAAAAGGG-ACGACGACAAG
31253 CTGACAAAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
43 13 0.17
44 8 0.10
45 56 0.73
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (44 bp):
ACAAATCAAAGACTCTCGGTCAAAAAGGGACGACGACAAGTTCA
Found at i:31340 original size:38 final size:37
Alignment explanation
Indices: 31246--31389 Score: 207
Period size: 37 Copynumber: 3.9 Consensus size: 37
31236 AAAGGGCACG
* **
31246 CGACAAGCTGACAAAATGTGTCGATCGCCATGTCGCT
1 CGACAAGCTGACAAAATGTGTCGACCGCCACATCGCT
*
31283 CGACAAGCTGACAAAATGTGTCGACCGCCACATCACT
1 CGACAAGCTGACAAAATGTGTCGACCGCCACATCGCT
* * *
31320 CGACAAAGCTGACAAGATGTGTCGACCGCCACATTGTT
1 CGAC-AAGCTGACAAAATGTGTCGACCGCCACATCGCT
*
31358 CGACAAGTTGACAAAATGTGTCGACCGCCACA
1 CGACAAGCTGACAAAATGTGTCGACCGCCACA
31390 AGCCACCTCA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
37 63 0.66
38 33 0.34
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (37 bp):
CGACAAGCTGACAAAATGTGTCGACCGCCACATCGCT
Found at i:31340 original size:75 final size:74
Alignment explanation
Indices: 31246--31389 Score: 216
Period size: 75 Copynumber: 1.9 Consensus size: 74
31236 AAAGGGCACG
* **
31246 CGACAAGCTGACAAAATGTGTCGATCGCCATGTCGCTCGACAAGCTGACAAAATGTGTCGACCGC
1 CGACAAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACAAGCTGACAAAATGTGTCGACCGC
31311 CACATCACT
66 CACATCACT
* * * *
31320 CGACAAAGCTGACAAGATGTGTCGACCGCCACATTGTTCGACAAGTTGACAAAATGTGTCGACCG
1 CGAC-AAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACAAGCTGACAAAATGTGTCGACCG
31385 CCACA
65 CCACA
31390 AGCCACCTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 4 0.06
75 58 0.94
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (74 bp):
CGACAAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACAAGCTGACAAAATGTGTCGACCGC
CACATCACT
Found at i:31529 original size:59 final size:59
Alignment explanation
Indices: 31438--31566 Score: 222
Period size: 59 Copynumber: 2.2 Consensus size: 59
31428 CCAATTAACT
* **
31438 AAAAAAAAAAGAGTTTCCCTTCTACCCATAGAAATTGAAATTCAAAATGTTGAATTTCA
1 AAAAAAAAAAAAGTTTCCCCCCTACCCATAGAAATTGAAATTCAAAATGTTGAATTTCA
*
31497 AAAAAAAAAAAAGTTTCCCCCCTACCCATAGAAATTGAAATTCAAAATGTTGAATTTCC
1 AAAAAAAAAAAAGTTTCCCCCCTACCCATAGAAATTGAAATTCAAAATGTTGAATTTCA
31556 AAAAAAAAAAA
1 AAAAAAAAAAA
31567 GATTAAAAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 66 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (59 bp):
AAAAAAAAAAAAGTTTCCCCCCTACCCATAGAAATTGAAATTCAAAATGTTGAATTTCA
Found at i:31941 original size:23 final size:23
Alignment explanation
Indices: 31915--31969 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
31905 CTTGGCGCCT
31915 GACCACTTACAAGCCTAGCGACC
1 GACCACTTACAAGCCTAGCGACC
* *
31938 GACCACTTACAAGCCTGGCGCCC
1 GACCACTTACAAGCCTAGCGACC
31961 GACCACTTA
1 GACCACTTA
31970 TGACCACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.40, G:0.18, T:0.15
Consensus pattern (23 bp):
GACCACTTACAAGCCTAGCGACC
Found at i:32047 original size:26 final size:26
Alignment explanation
Indices: 32009--32130 Score: 149
Period size: 26 Copynumber: 4.7 Consensus size: 26
31999 GCCAGCTGGC
* *
32009 ACTCCACATGTGACCTCCAATGTACG
1 ACTCCACACGTGACCTCCAACGTACG
32035 ACTCCACACGTGACCTCCAACGTACG
1 ACTCCACACGTGACCTCCAACGTACG
* *
32061 ACTCCTCACGTGACCTCCAACGGAC-
1 ACTCCACACGTGACCTCCAACGTACG
* *
32086 ACCTTCAACACGTGACCTCCGAA-GTACA
1 A-C-TCCACACGTGACCTCC-AACGTACG
32114 ACTCCACACGTGACCTC
1 ACTCCACACGTGACCTC
32131 GCGCGTGCGA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.01
26 62 0.74
27 18 0.21
28 3 0.04
ACGTcount: A:0.27, C:0.40, G:0.15, T:0.18
Consensus pattern (26 bp):
ACTCCACACGTGACCTCCAACGTACG
Found at i:42867 original size:15 final size:15
Alignment explanation
Indices: 42847--42877 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42837 AGTCTCCAGA
42847 AGATCCAATTATTGG
1 AGATCCAATTATTGG
42862 AGATCCAATTATTGG
1 AGATCCAATTATTGG
42877 A
1 A
42878 TTATTGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (15 bp):
AGATCCAATTATTGG
Found at i:44462 original size:5 final size:5
Alignment explanation
Indices: 44452--44521 Score: 56
Period size: 5 Copynumber: 13.6 Consensus size: 5
44442 AAAAATATTT
*
44452 TTTTC TTTTC -TTT- TTTTC TTTTCC GTTTTTC TATTCC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTT-C --TTTTC T-TTTC TTTTC TTTTC
*
44499 TTTTTC TTTT- TTTCC TTTTC TTT
1 -TTTTC TTTTC TTTTC TTTTC TTT
44522 CTTCTTCCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
4 9 0.17
5 29 0.55
6 10 0.19
7 1 0.02
8 4 0.08
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:44465 original size:13 final size:13
Alignment explanation
Indices: 44449--44521 Score: 74
Period size: 13 Copynumber: 5.2 Consensus size: 13
44439 AAAAAAAATA
44449 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
44462 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
** *
44475 CGTTTTTCTATTCC
1 TTTTTTTCT-TTTC
44489 TTTTCTTTTCTTTTTC
1 -TTT-TTTTC-TTTTC
44505 TTTTTTTCCTTTTC
1 TTTTTTT-CTTTTC
44519 TTT
1 TTT
44522 CTTCTTCCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
13 20 0.41
14 15 0.31
15 5 0.10
16 8 0.16
17 1 0.02
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:44498 original size:29 final size:25
Alignment explanation
Indices: 44465--44531 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 25
44455 TCTTTTCTTT
44465 TTTTCTTTTCCGTTTTTCTATTCCTTTTC
1 TTTTCTTTTCC--TTTT-T-TTCCTTTTC
*
44494 TTTTCTTTTTCTTTTTTTCCTTTTC
1 TTTTCTTTTCCTTTTTTTCCTTTTC
44519 -TTTCTTCTTCCTT
1 TTTTCTT-TTCCTT
44532 CTTCAAAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 6 0.17
25 14 0.40
26 1 0.03
27 4 0.11
29 10 0.29
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.73
Consensus pattern (25 bp):
TTTTCTTTTCCTTTTTTTCCTTTTC
Found at i:44518 original size:6 final size:6
Alignment explanation
Indices: 44451--44509 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
44441 AAAAAATATT
* * * *
44451 TTTTTC TTTTCTT TTTTTC TTTTCC GTTTTTC -TATTC CTTTTC -TTTTC
1 TTTTTC TTTT-TC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC
44499 TTTTTC TTTTT
1 TTTTTC TTTTT
44510 TTCCTTTTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 9 0.21
6 24 0.56
7 10 0.23
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:46005 original size:17 final size:18
Alignment explanation
Indices: 45983--46018 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
45973 TTTAAAATAT
45983 ATATTAAAAATAA-TAAA
1 ATATTAAAAATAATTAAA
46000 ATATTAAAAATAATTAAA
1 ATATTAAAAATAATTAAA
46018 A
1 A
46019 AAAGCCACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATATTAAAAATAATTAAA
Found at i:46021 original size:21 final size:21
Alignment explanation
Indices: 45974--46021 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 21
45964 TTATTAAAAT
*
45974 TTAAAATATATATTAAAAATAA
1 TTAAAA-AAATATTAAAAATAA
45996 -T---AAAATATTAAAAATAA
1 TTAAAAAAATATTAAAAATAA
46013 TTAAAAAAA
1 TTAAAAAAA
46022 GCCACGTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 9
0.68 0.03 0.29
Matches are distributed among these distances:
17 14 0.67
18 2 0.10
21 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAAAAAATATTAAAAATAA
Found at i:46154 original size:66 final size:66
Alignment explanation
Indices: 46048--46181 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
46038 AACGGAAAAA
46048 TGGACTTAACGGGAACTTAACAGCGCGGTAGTTCAAATGCGCTGATAGACTAAAAAAGTACTAAA
1 TGGACTTAACGGGAACTTAACAGCGCGGTAGTTCAAATGCGCTGATAGACTAAAAAAGTACTAAA
46113 T
66 T
*
46114 TGGACTTAACGGGAACTTAACAGCGCGGTAGTTCAAATGCGTTGATAGACTAAAAAAGTACTAAA
1 TGGACTTAACGGGAACTTAACAGCGCGGTAGTTCAAATGCGCTGATAGACTAAAAAAGTACTAAA
46179 T
66 T
46180 TG
1 TG
46182 AATCATTAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (66 bp):
TGGACTTAACGGGAACTTAACAGCGCGGTAGTTCAAATGCGCTGATAGACTAAAAAAGTACTAAA
T
Found at i:52884 original size:21 final size:20
Alignment explanation
Indices: 52825--52884 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 20
52815 ACGGAAAATA
*
52825 AATTTTTTTTAGAGAAAACAC
1 AATTTTTTTTAAAG-AAACAC
* *
52846 AA-TTTTTTTAACCGGAAACCC
1 AATTTTTTTTAA--AGAAACAC
52867 TAATTTTTTTTAAAGAAA
1 -AATTTTTTTTAAAGAAA
52885 AAGCGGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
20 8 0.26
21 11 0.35
22 3 0.10
23 9 0.29
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (20 bp):
AATTTTTTTTAAAGAAACAC
Found at i:59376 original size:30 final size:30
Alignment explanation
Indices: 59342--59436 Score: 82
Period size: 36 Copynumber: 3.0 Consensus size: 30
59332 CTAAGCACCG
*
59342 TGATCGTGATGCTAAGCACCATAGGTTGGA
1 TGATCATGATGCTAAGCACCATAGGTTGGA
* * *
59372 TGATCATCACGCTAAGGGCAAGCGCGGTAGGTTGGA
1 TGATCATGATGCTAA--GC-A-C-C-ATAGGTTGGA
* *
59408 TGATCATGATGCTAACCACCATAAGTTGG
1 TGATCATGATGCTAAGCACCATAGGTTGG
59437 CTGGATATGC
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
30 19 0.38
31 1 0.02
32 3 0.06
33 2 0.04
34 2 0.04
35 1 0.02
36 22 0.44
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (30 bp):
TGATCATGATGCTAAGCACCATAGGTTGGA
Found at i:63726 original size:17 final size:18
Alignment explanation
Indices: 63698--63732 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
63688 CGACACCCTT
*
63698 AACCTAAAACTAGAGAAA
1 AACCTAAAACTAAAGAAA
63716 AACCT-AAACTAAAGAAA
1 AACCTAAAACTAAAGAAA
63733 GGTAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.63, C:0.17, G:0.09, T:0.11
Consensus pattern (18 bp):
AACCTAAAACTAAAGAAA
Found at i:76087 original size:21 final size:21
Alignment explanation
Indices: 76054--76102 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
76044 AAGAATTGTA
**
76054 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
76074 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
76095 GCATTCCT
1 GC-TTCCT
76103 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:80439 original size:18 final size:17
Alignment explanation
Indices: 80412--80447 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
80402 TTTCTCTTCA
*
80412 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCCAGT
80429 TCTAGTTTTTCTTCCAGT
1 TCTA-TTTTTCTTCCAGT
80447 T
1 T
80448 TTAGATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.11, C:0.19, G:0.08, T:0.61
Consensus pattern (17 bp):
TCTATTTTTCTTCCAGT
Found at i:81500 original size:17 final size:18
Alignment explanation
Indices: 81470--81504 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
81460 TAAAAAAGAA
81470 AAAATTTGTTTTTGCGTT
1 AAAATTTGTTTTTGCGTT
81488 AAAATTT-TTTTTGCGTT
1 AAAATTTGTTTTTGCGTT
81505 TTCTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (18 bp):
AAAATTTGTTTTTGCGTT
Found at i:86264 original size:27 final size:27
Alignment explanation
Indices: 86234--86285 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
86224 GCATTAGGGT
86234 CATTCAGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
*
86261 CATTCAGGGGCATTTTTGTCATTTT
1 CATTCAGGGGCATTTTGGTCATTTT
86286 GATTCCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.46
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTTTA
Found at i:90514 original size:15 final size:16
Alignment explanation
Indices: 90494--90523 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
90484 AGAGAACATT
90494 AAAAAAACA-TTTTTG
1 AAAAAAACACTTTTTG
90509 AAAAAAACACTTTTT
1 AAAAAAACACTTTTT
90524 ATTACATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAAAAACACTTTTTG
Found at i:93392 original size:48 final size:45
Alignment explanation
Indices: 93332--93935 Score: 279
Period size: 48 Copynumber: 13.8 Consensus size: 45
93322 CTTGTCTCCA
* *
93332 CTTTTCCAAAATTGCCCTTCCTCATCGGAAGGTGTTGTCTAGGTCTG
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTA--TCTG
* * * *
93379 CTATTTCCCAAATTGCTCTTCCTCATCGGAAAGTGTTGTCTAACTCTA
1 CT-TTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCT-A-TCTG
* *
93427 CTTTTTCCCAAATTGCTCTTCCCCAATCGGAAGGTGTTG-CT-T-AG
1 C-TTTTCCCAAATTGCCCTTCCCC-ATCGGAAGGTGTTGTCTATCTG
**** * **
93471 -TTTTCCTGTTTTGCCCTTCCCCACCGGAAGGTGTTGT-T-TAAG
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTATCTG
** * * *
93513 --TTTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTATCTAAGTCTA
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCT-A-TCTG
* * *
93558 CTTTTTCCGAAATTACCCTTCCCCATCGGAAGGTGTTGT-T-T-AG
1 C-TTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTATCTG
** * *
93601 --TTTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTA
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCT-A-TCTG
* * *
93646 CTTTTTCCGAAATTACCCTTCCCCATCGGAAGGTGTTGT-T-T-AG
1 C-TTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTATCTG
** **** * **
93689 --TTTCCCAGTTTGCCCTTCCTGGCCGGAAGATGTTGT-T-TAAG
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTATCTG
* * *
93730 --TTTCCTAATTTGCCCTTTCCCATCGGAAGGTGTTGT-T-T-TAG
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTATCT-G
* ** * * *
93771 -TTTTTCCAGCTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAGTCTA
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCT-A-TCTG
* ** * *
93817 CATTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTCGT-T-T-AG
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTATCTG
** *
93859 -TTTT-CCAGCTTGCCCTTCCCCACCGGAAGGTGTTGTCTA----
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTATCTG
* * **
93898 CATTTCGCAGTTTGCCCTTCCCCATCGGAAGGTGTTGT
1 CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGT
93936 TTAGTTTTCC
Statistics
Matches: 435, Mismatches: 88, Indels: 74
0.73 0.15 0.12
Matches are distributed among these distances:
40 92 0.21
41 112 0.26
42 49 0.11
43 2 0.00
44 3 0.01
45 2 0.00
46 2 0.00
47 36 0.08
48 122 0.28
49 15 0.03
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (45 bp):
CTTTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTCTATCTG
Found at i:93517 original size:41 final size:40
Alignment explanation
Indices: 93439--93978 Score: 376
Period size: 41 Copynumber: 12.7 Consensus size: 40
93429 TTTTCCCAAA
* * *
93439 TTGCTCTTCCCCAATCGGAAGGTGTTGCTT-AGTTTTCCTGTT
1 TTGCCCTTCCCC-ATCGGAAGGTGTTGTTTAAG-TTTCCAG-T
*
93481 TTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTTCCCAGT
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTT-CCAGT
* * * **
93522 TTGCCCTTCCTCATCGGAAGGTGTTATCTAAGTCTACTTTTTCCGAAA
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG-------TTTCC-AGT
*
93570 TTACCCTTCCCCATCGGAAGGTGTTGTTT-AGTTTCCCAGT
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTT-CCAGT
* * **
93610 TTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTTTCCGAAA
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG-------TTTCC-AGT
*
93658 TTACCCTTCCCCATCGGAAGGTGTTGTTT-AGTTTCCCAGT
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTT-CCAGT
**** * *
93698 TTGCCCTTCCTGGCCGGAAGATGTTGTTTAAGTTTCCTAAT
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTTCC-AGT
* * *
93739 TTGCCCTTTCCCATCGGAAGGTGTTGTTTTAGTTTTTCCAGC
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG--TTTCCAGT
* * *
93781 TTGCCCTTCCTCACCGGAAGGTGTTGTCTAAGTCTACATTTCCCAGT
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG------TTT-CCAGT
* *
93828 TTGCCCTTCCCCATCGGAAGGTGTCGTTT-AGTTTTCCAGC
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG-TTTCCAGT
* *
93868 TTGCCCTTCCCCACCGGAAGGTGTTGTCTACA-TTTCGCAGT
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTA-AGTTTC-CAGT
93909 TTGCCCTTCCCCATCGGAAGGTGTTGTTT-AGTTTTCCTA-T
1 TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG-TTTCC-AGT
* *
93949 CTTGCCCTTCCACA-CTAGAAGGTGTTGTTT
1 -TTGCCCTTCCCCATC-GGAAGGTGTTGTTT
93979 GCTCTTCTTT
Statistics
Matches: 396, Mismatches: 64, Indels: 77
0.74 0.12 0.14
Matches are distributed among these distances:
39 1 0.00
40 96 0.24
41 148 0.37
42 45 0.11
43 5 0.01
46 5 0.01
47 37 0.09
48 59 0.15
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTTCCAGT
Found at i:93630 original size:88 final size:87
Alignment explanation
Indices: 93484--93976 Score: 546
Period size: 88 Copynumber: 5.7 Consensus size: 87
93474 TCCTGTTTTG
* * *
93484 CCCTTCCCCACCGGAAGGTGTTGTTTAAGTTTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTAT
1 CCCTTCCCCATCGGAAGGTGTTGTTT-AGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGT
93549 CTAAGTCTACTTTTTCCGAAATTA
65 CTAAGTCTAC-TTTTCCGAAATTA
*
93573 CCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTC
1 CCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTC
93638 TAAGTCTACTTTTTCCGAAATTA
66 TAAGTCTAC-TTTTCCGAAATTA
** * *
93661 CCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTGGCCGGAAGATGTTGTT
1 CCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTC
* * *
93726 TAAG------TTTCCTAATTTG
66 TAAGTCTACTTTTCCGAAATTA
* * *
93742 CCCTTTCCCATCGGAAGGTGTTGTTTTAGTTTTTCCAGCTTGCCCTTCCTCACCGGAAGGTGTTG
1 CCCTTCCCCATCGGAAGGTGTTG-TTTAG-TTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGTTG
* * ** *
93807 TCTAAGTCTACATTTCCCAGTTTG
64 TCTAAGTCTACTTTTCCGAAATTA
* * * *
93831 CCCTTCCCCATCGGAAGGTGTCGTTTAGTTTTCCAGCTTGCCCTTCCCCACCGGAAGGTGTTGTC
1 CCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTC
** *
93896 T-A--C-A--TTT-CGCAGTTTG
66 TAAGTCTACTTTTCCG-AAATTA
* * **
93912 CCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTA-TCTTGCCCTTCCACACTAGAAGGTGTTG
1 CCCTTCCCCATCGGAAGGTGTTGTTTAG-TTTCCCAGT-TTGCCCTTCCTCACCGGAAGGTGTTG
93976 T
64 T
93977 TTGCTCTTCT
Statistics
Matches: 363, Mismatches: 30, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
80 1 0.00
81 67 0.18
82 34 0.09
83 36 0.10
84 1 0.00
86 1 0.00
87 37 0.10
88 130 0.36
89 56 0.15
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (87 bp):
CCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTC
TAAGTCTACTTTTCCGAAATTA
Found at i:93859 original size:170 final size:168
Alignment explanation
Indices: 93480--93976 Score: 602
Period size: 170 Copynumber: 2.9 Consensus size: 168
93470 GTTTTCCTGT
* *
93480 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTTCCCAGTTTGCCCTTCCTCATCGGAAGGTG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTG
* * * * *
93545 TTATCTAAGTCTACTTTTTCCGAAATTACCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGT
65 TTGTCTAAG-------TTTCC-AATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCAGC
* * *
93610 TTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTTTCCGAA
122 TTGCCCTTCCTCACCGGAAGGTGTTGTCTAAGTCTACTATTTCCCAA
* * ** *
93657 ATTACCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTGGCCGGAAGATGT
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGT
* *
93722 TGTTTAAGTTTCCTAATTTGCCCTTTCCCATCGGAAGGTGTTGTTTTAGTTTTTCCAGCTTGCCC
66 TGTCTAAGTTTCC-AATTTGCCCTTCCCCATCGGAAGGTGTTG-TTTAG-TTTTCCAGCTTGCCC
*
93787 TTCCTCACCGGAAGGTGTTGTCTAAGTCTAC-ATTTCCCAG
128 TTCCTCACCGGAAGGTGTTGTCTAAGTCTACTATTTCCCAA
* * * *
93827 TTTGCCCTTCCCCATCGGAAGGTGTCGTTTAGTTTTCCAGCTTGCCCTTCCCCACCGGAAGGTGT
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGT
* *
93892 TGTCTACA-TTTCGCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTATCTTGCCC
66 TGTCTA-AGTTTC-CAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCC-AGCTTGCCC
* **
93956 TTCCACACTAGAAGGTGTTGT
128 TTCCTCACCGGAAGGTGTTGT
93977 TTGCTCTTCT
Statistics
Matches: 280, Mismatches: 35, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
168 6 0.02
169 62 0.22
170 103 0.37
171 45 0.16
176 37 0.13
177 27 0.10
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (168 bp):
TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCACCGGAAGGTGT
TGTCTAAGTTTCCAATTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCAGCTTGCCCTTC
CTCACCGGAAGGTGTTGTCTAAGTCTACTATTTCCCAA
Found at i:94061 original size:50 final size:50
Alignment explanation
Indices: 93992--94576 Score: 620
Period size: 50 Copynumber: 11.8 Consensus size: 50
93982 CTTCTTTTTG
**
93992 CAAAATGCCCCTTCCCGGTCAAAAGGTCACTGTTTTCTTTTTCTGTTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTTTCTGTTTCC
* * * * *
94042 CAAAATGCCCTTTCACGGTCGGAAGGTCATTGTTTTCTATATCTGTTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTTTCTGTTTCC
* ** * * * *
94092 GAAAAAACCCCTTCCCAGTCGGAAGGTCATTGTTTTCTATATCTGTTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTTTCTGTTTCC
*
94142 C-AAATAGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATT-TGTTACC
1 CAAAAT-GCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTT-TTCTGTTTCC
* * * *
94192 AAAAATGCCTCC-TCCTGGTCGGAAGGTCACTGTTTCCTTTATCTGTTTCC
1 CAAAATGCC-CCTTCCCGGTCGGAAGGTCACTGTTTTCTTTTTCTGTTTCC
* *
94242 CAAAAAGCCCCTTCCCGGTCGGAAGGTCACTATTTTCTTTATT-TGTTT-C
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTT-TTCTGTTTCC
* * * * *
94291 CAAAATGCCCCTTCCCGGTCAGAAGGTCCCTGTTTTCTTTATATATTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTTTCTGTTTCC
* * * *
94341 CAAAATGCCTCTT-CCGGATCAGAAGGTCCCTGTTTTCTATATT-TGTTTCC
1 CAAAATGCCCCTTCCCGG-TCGGAAGGTCACTGTTTTCT-TTTTCTGTTTCC
* * *
94391 CAAAATGCCCCTTCCCAGTCGAAAGGTCCCTGTTTTCTTTATTC-GTTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTT-TTCTGTTTCC
* *
94441 TAAAATGCCCCTTCCCGGTCGGAAGGTC-CATGTTCTCTTTATT-TGTTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCAC-TGTTTTCTTT-TTCTGTTTCC
* * * * *
94491 CAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTCTT-T-ATTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTT-TTCTGTTTCC
*
94540 CAAAATGCCCCTTCCCGGTCGGAAGGTC-CAGTTTTCT
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCT
94577 CTTCACATTT
Statistics
Matches: 458, Mismatches: 60, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
48 10 0.02
49 83 0.18
50 351 0.77
51 14 0.03
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (50 bp):
CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTTTCTGTTTCC
Found at i:94118 original size:100 final size:99
Alignment explanation
Indices: 93992--94576 Score: 691
Period size: 100 Copynumber: 5.9 Consensus size: 99
93982 CTTCTTTTTG
** * * *
93992 CAAAATGCCCCTTCCCGGTCAAAAGGTCACTGTTTTCTTTTTCTGTTTCCCAAAATGCCCTTTCA
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAATGCCCCTTCC
* * *
94057 CGGTCGGAAGGTCATTGTTTTCTATATCTGTTTC
66 CGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
** * * *
94091 CGAAAAAACCCCTTCCCAGTCGGAAGGTCATTGTTTTCTATATCTGTTTCCC-AAATAGCCCCTT
1 C-AAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAAT-GCCCCTT
*
94155 CCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTAC
64 CCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
* * *
94191 CAAAAATGCCTCC-TCCTGGTCGGAAGGTCACTGTTTCCTTTATCTGTTTCCCAAAAAGCCCCTT
1 C-AAAATGCC-CCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAATGCCCCTT
*
94255 CCCGGTCGGAAGGTCACTATTTTCTTTATTTGTTTC
64 CCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
* * * * *
94291 CAAAATGCCCCTTCCCGGTCAGAAGGTCCCTGTTTTCTTTATATATTTCCCAAAATGCCTCTT-C
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAATGCCCCTTCC
* * *
94355 CGGATCAGAAGGTCCCTGTTTTCTATATTTGTTTCC
66 CGG-TCGGAAGGTCACTGTTTTCTTTATTTGTTT-C
* * * *
94391 CAAAATGCCCCTTCCCAGTCGAAAGGTCCCTGTTTTCTTTAT-TCGTTTCCTAAAATGCCCCTTC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCT-GTTTCCCAAAATGCCCCTTC
*
94455 CCGGTCGGAAGGTC-CATGTTCTCTTTATTTGTTTCC
65 CCGGTCGGAAGGTCAC-TGTTTTCTTTATTTGTTT-C
* * * * *
94491 CAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTC-TT-TCTTTATTCCCAAAATGCCCCTTC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGT-TTCCCAAAATGCCCCTTC
*
94554 CCGGTCGGAAGGTC-CAGTTTTCT
65 CCGGTCGGAAGGTCACTGTTTTCT
94577 CTTCACATTT
Statistics
Matches: 419, Mismatches: 55, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
98 14 0.03
99 119 0.28
100 277 0.66
101 9 0.02
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (99 bp):
CAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAATGCCCCTTCC
CGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
Found at i:94448 original size:249 final size:248
Alignment explanation
Indices: 93992--94576 Score: 716
Period size: 249 Copynumber: 2.3 Consensus size: 248
93982 CTTCTTTTTG
** * * *
93992 CAAAATGCCCCTTCCCGGTCAAAAGGTCACTGTTTTCTTTTTCTGTTTCCCAAAATGCCCTTTCA
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTTCTTTTT-TGTTT-CCAAAATGCCCCTTCC
** * * * * *
94057 CGGTCGGAAGGTCATTGTTTTCTATATCTGTTTCCGAAAAAACCCCTTCCCAGTCGGAAGGTCAT
64 CGGTCGGAAGGTCCCTGTTTTCTATATATATTTCCCAAAAAACCCCTTCCCAGTCAGAAGGTCAC
* * *
94122 TGTTTTCTATATCTGTTTCCCAAATAGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTG
129 TGTTTTCTATATCTGTTTCCCAAATAGCCCCTTCCCAGTCGAAAGGTCACTGTTTTCTTTATTCG
*
94187 TTACCAAAAATGCCTCC-TCCTGGTCGGAAGGT-CACTGTT-TCCTTTATCTGTTTCC
194 TTACCAAAAATGCC-CCTTCCCGGTCGGAAGGTCCA-TGTTCT-CTTTATCTGTTTCC
*
94242 CAAAAAGCCCCTTCCCGGTCGGAAGGTCACTATTTTCTTTATTTGTTTCCAAAATGCCCCTTCCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTTCTTT-TTTGTTTCCAAAATGCCCCTTCCC
* * ** * * *
94307 GGTCAGAAGGTCCCTGTTTTCTTTATATATTTCCCAAAATGCCTCTT-CCGGATCAGAAGGTCCC
65 GGTCGGAAGGTCCCTGTTTTCTATATATATTTCCCAAAAAACCCCTTCCCAG-TCAGAAGGTCAC
* *
94371 TGTTTTCTATATTTGTTTCCCAAA-ATGCCCCTTCCCAGTCGAAAGGTCCCTGTTTTCTTTATTC
129 TGTTTTCTATATCTGTTTCCCAAATA-GCCCCTTCCCAGTCGAAAGGTCACTGTTTTCTTTATTC
* * *
94435 GTTTCCTAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTCTCTTTATTTGTTTCC
193 GTTACCAAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTCTCTTTATCTGTTTCC
* * * * *
94491 CAAAATGCCCCTTCCTGGTTGGAAGGTC-CCAGTTTTCTTTCTTTATTCCCAAAATGCCCCTTCC
1 CAAAATGCCCCTTCCCGGTCGGAAGGTCACTA-TTTTCTTT-TTTGTTTCCAAAATGCCCCTTCC
*
94555 CGGTCGGAAGGT-CCAGTTTTCT
64 CGGTCGGAAGGTCCCTGTTTTCT
94577 CTTCACATTT
Statistics
Matches: 290, Mismatches: 38, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
248 17 0.06
249 227 0.78
250 44 0.15
251 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (248 bp):
CAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTTCTTTTTTGTTTCCAAAATGCCCCTTCCCG
GTCGGAAGGTCCCTGTTTTCTATATATATTTCCCAAAAAACCCCTTCCCAGTCAGAAGGTCACTG
TTTTCTATATCTGTTTCCCAAATAGCCCCTTCCCAGTCGAAAGGTCACTGTTTTCTTTATTCGTT
ACCAAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTCTCTTTATCTGTTTCC
Found at i:97429 original size:29 final size:30
Alignment explanation
Indices: 97374--97439 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
97364 AAGTATTTTC
*
97374 CCTCTAAAAGGAAAAAGAGAGTGTTAGTAA
1 CCTCTAAAAGGAAAAAGAGAGAGTTAGTAA
*
97404 CCTCTCAAAA-GAAAAA-AGGGAGTTAGTAA
1 CCTCT-AAAAGGAAAAAGAGAGAGTTAGTAA
*
97433 CCCCTAA
1 CCTCTAA
97440 GCCATGAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.06
29 15 0.47
30 11 0.34
31 4 0.12
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (30 bp):
CCTCTAAAAGGAAAAAGAGAGAGTTAGTAA
Found at i:98735 original size:76 final size:74
Alignment explanation
Indices: 98592--98764 Score: 240
Period size: 76 Copynumber: 2.3 Consensus size: 74
98582 TATCAAAGTT
* * * *
98592 GACTGGAAACAGGTCATCTTTCAGCAATTATTTTTCGACTGGAAACATGTCATCTTTCAGCAATT
1 GACTGGAAACAGGTCGTCTTTCAGCAATTATGTTTCGACTGGAAACAAGTCATCTTTCAACAATT
*
98657 ATCGAGATC
66 ATCAAGATC
* *
98666 GACTGGAAACAGGTTGTCTTTCAGCACTTATCAAGTTT-GACTGGAAACAAGTCATCTTTCAACA
1 GACTGGAAACAGGTCGTCTTTCAGCAATTAT---GTTTCGACTGGAAACAAGTCATCTTTCAACA
*
98730 GTTATCAAGATC
63 ATTATCAAGATC
98742 GACTGGAAACAGGTCGTCTTTCA
1 GACTGGAAACAGGTCGTCTTTCA
98765 ACAGTTTTCG
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
74 28 0.32
76 56 0.64
77 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (74 bp):
GACTGGAAACAGGTCGTCTTTCAGCAATTATGTTTCGACTGGAAACAAGTCATCTTTCAACAATT
ATCAAGATC
Found at i:98770 original size:38 final size:38
Alignment explanation
Indices: 98592--98764 Score: 206
Period size: 38 Copynumber: 4.6 Consensus size: 38
98582 TATCAAAGTT
***
98592 GACTGGAAACAGGTCATCTTTCAGCAATTAT--TTTTC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCAAGATC
* *
98628 GACTGGAAACATGTCATCTTTCAGCAATTATCGAGATC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCAAGATC
** * * *
98666 GACTGGAAACAGGTTGTCTTTCAGCACTTATCAAGTTT
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCAAGATC
* * *
98704 GACTGGAAACAAGTCATCTTTCAACAGTTATCAAGATC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCAAGATC
*
98742 GACTGGAAACAGGTCGTCTTTCA
1 GACTGGAAACAGGTCATCTTTCA
98765 ACAGTTTTCG
Statistics
Matches: 115, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
36 30 0.26
38 85 0.74
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (38 bp):
GACTGGAAACAGGTCATCTTTCAGCAATTATCAAGATC
Found at i:98823 original size:15 final size:16
Alignment explanation
Indices: 98799--98891 Score: 84
Period size: 15 Copynumber: 5.7 Consensus size: 16
98789 GGGCATTCCA
98799 ACAACTTTTCA-ATTT
1 ACAACTTTTCACATTT
*
98814 ACAACCTTTCAGCATTT
1 ACAACTTTTCA-CATTT
98831 ACAACTTTTCAGCA-TT
1 ACAACTTTTCA-CATTT
* *
98847 CCAACTTTTC-GATTT
1 ACAACTTTTCACATTT
*
98862 ACAACTTTTCAGCATTCCA
1 ACAACTTTTCA-CATT--T
98881 ACAACTTTTCA
1 ACAACTTTTCA
98892 TTTTTCAGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.02
15 21 0.33
16 11 0.17
17 20 0.31
19 11 0.17
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.39
Consensus pattern (16 bp):
ACAACTTTTCACATTT
Found at i:98832 original size:17 final size:17
Alignment explanation
Indices: 98799--99053 Score: 109
Period size: 17 Copynumber: 14.6 Consensus size: 17
98789 GGGCATTCCA
98799 ACAACTTTTCA--ATTT
1 ACAACTTTTCAGCATTT
*
98814 ACAACCTTTCAGCATTT
1 ACAACTTTTCAGCATTT
98831 ACAACTTTTCAGCA-TT
1 ACAACTTTTCAGCATTT
*
98847 CCAACTTTTC-G-ATTT
1 ACAACTTTTCAGCATTT
*
98862 ACAACTTTTCAGCATTCCA
1 ACAACTTTTCAGCATT--T
* *
98881 ACAACTTTTCATTTTTCAGTT
1 ACAACTTTTCA----GCATTT
** ***** *
98902 ACTCCCAAGGGGAGGCATTCC
1 AC-AAC-TTTTCA-GCATT-T
98923 AACAACTTTTCA--ATTT
1 A-CAACTTTTCAGCATTT
*
98939 ACAACCTTTCAGCATTT
1 ACAACTTTTCAGCATTT
* *
98956 ACAACTTTTCACCATTCCA
1 ACAACTTTTCAGCATT--T
98975 ACAACTTTTC-G-ATTT
1 ACAACTTTTCAGCATTT
*
98990 ACAACTTTTCAGCATTCCA
1 ACAACTTTTCAGCATT--T
99009 ACAACTTTTCA--ATTT
1 ACAACTTTTCAGCATTT
* *
99024 ATAACTTTTCAGCATTCCA
1 ACAACTTTTCAGCATT--T
99043 ACAACTTTTCA
1 ACAACTTTTCA
99054 ATTTTCAGTT
Statistics
Matches: 175, Mismatches: 38, Indels: 50
0.67 0.14 0.19
Matches are distributed among these distances:
14 1 0.01
15 51 0.29
16 14 0.08
17 53 0.30
19 42 0.24
20 4 0.02
21 4 0.02
22 2 0.01
23 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.38
Consensus pattern (17 bp):
ACAACTTTTCAGCATTT
Found at i:98976 original size:51 final size:52
Alignment explanation
Indices: 98917--99019 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 52
98907 CAAGGGGAGG
*
98917 CATTCCAACAACTTTTCAATTTACAACCTTTCAGCATT-TACAACTTTTCAC
1 CATTCCAACAACTTTTCAATTTACAACCTTTCAGCATTCAACAACTTTTCAC
* *
98968 CATTCCAACAACTTTTCGATTTACAACTTTTCAGCATTCCAACAACTTTTCA
1 CATTCCAACAACTTTTCAATTTACAACCTTTCAGCATT-CAACAACTTTTCA
99020 ATTTATAACT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 36 0.77
53 11 0.23
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (52 bp):
CATTCCAACAACTTTTCAATTTACAACCTTTCAGCATTCAACAACTTTTCAC
Found at i:98980 original size:19 final size:19
Alignment explanation
Indices: 98956--99053 Score: 86
Period size: 19 Copynumber: 5.6 Consensus size: 19
98946 TTCAGCATTT
98956 ACAACTTTTCACCATTCCA
1 ACAACTTTTCACCATTCCA
* *
98975 ACAACTTTT--CGATT--T
1 ACAACTTTTCACCATTCCA
*
98990 ACAACTTTTCAGCATTCCA
1 ACAACTTTTCACCATTCCA
*
99009 ACAACTTTTCA--ATT--T
1 ACAACTTTTCACCATTCCA
* *
99024 ATAACTTTTCAGCATTCCA
1 ACAACTTTTCACCATTCCA
99043 ACAACTTTTCA
1 ACAACTTTTCA
99054 ATTTTCAGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
15 19 0.31
17 13 0.21
19 30 0.48
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.38
Consensus pattern (19 bp):
ACAACTTTTCACCATTCCA
Found at i:98995 original size:34 final size:34
Alignment explanation
Indices: 98952--99057 Score: 185
Period size: 34 Copynumber: 3.1 Consensus size: 34
98942 ACCTTTCAGC
* *
98952 ATTTACAACTTTTCACCATTCCAACAACTTTTCG
1 ATTTACAACTTTTCAGCATTCCAACAACTTTTCA
98986 ATTTACAACTTTTCAGCATTCCAACAACTTTTCA
1 ATTTACAACTTTTCAGCATTCCAACAACTTTTCA
*
99020 ATTTATAACTTTTCAGCATTCCAACAACTTTTCA
1 ATTTACAACTTTTCAGCATTCCAACAACTTTTCA
99054 ATTT
1 ATTT
99058 TCAGTTACTC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (34 bp):
ATTTACAACTTTTCAGCATTCCAACAACTTTTCA
Found at i:99517 original size:27 final size:27
Alignment explanation
Indices: 99494--99544 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
99484 TCTTTTTTGG
99494 CATT-AGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGCATTTTGGTCATTTTTA
99520 CATTCAGGGGCATTTTGGTCATTTT
1 CATTCAGGGGCATTTTGGTCATTTT
99545 GATTCCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.45
Consensus pattern (27 bp):
CATTCAGGGGCATTTTGGTCATTTTTA
Found at i:100014 original size:12 final size:12
Alignment explanation
Indices: 99997--100027 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
99987 ATATGTTTTA
99997 TTGCTTATTCAT
1 TTGCTTATTCAT
100009 TTGCTTATTCAT
1 TTGCTTATTCAT
*
100021 TTCCTTA
1 TTGCTTA
100028 CACCAGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.58
Consensus pattern (12 bp):
TTGCTTATTCAT
Found at i:102751 original size:48 final size:47
Alignment explanation
Indices: 102687--102819 Score: 189
Period size: 48 Copynumber: 2.8 Consensus size: 47
102677 TCTTGTTTCC
*
102687 ACTTTTCCAAAATTGCCCTTCCTCATCGGAAGGTGTTGTCT-AGTTCT
1 ACTTTTCCCAAATTGCCCTTCCTCATCGGAAGGTGTTGTCTAAG-TCT
102734 ACTTTTCCGCAAATTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCT
1 ACTTTTCC-CAAATTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCT
* *
102782 ACTTTTTCCCAAATTTCTCTT-CTCCATCGGAAGGTGTT
1 AC-TTTTCCCAAATTGCCCTTCCT-CATCGGAAGGTGTT
102820 CTTTAGTTTC
Statistics
Matches: 79, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
47 10 0.13
48 61 0.77
49 8 0.10
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (47 bp):
ACTTTTCCCAAATTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCT
Found at i:102934 original size:41 final size:40
Alignment explanation
Indices: 102800--103279 Score: 297
Period size: 41 Copynumber: 11.6 Consensus size: 40
102790 CCAAATTTCT
* * *
102800 CTTCTCCATCGGAAGGTGTTCTTTAGTTTCCCAGTATG--
1 CTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCC
* * * * *
102838 C--GCCCATCGGAAGTTGTTGCTTAGTTTTCCTGTTTTGCC
1 CTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAG-TTTGCC
* **
102877 CTTCCCCACCAAAAGGTGTTGTTTAAGTTTCCCAGTTTGCC
1 CTTCCCCATCGGAAGGTGTTGTTT-AGTTTCCCAGTTTGCC
* * * * **
102918 CTTTCTCATCGGAAGGTGTCGTCTAAGTCTACTTTTTCCCAAATTGCC
1 CTTCCCCATCGGAA-G-GT-GT-T--GTTTA--GTTTCCCAGTTTGCC
*
102966 CTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAATTTGCC
1 CTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCC
** *
103006 CTTCCCGGTCGGAAGATGTTGTTTAAGTTTCCCAGTTTGCC
1 CTTCCCCATCGGAAGGTGTTGTTT-AGTTTCCCAGTTTGCC
* * **
103047 CTTCCCCATGGGAAGGTGTTGTTTAGTTTTTCCAACTTGCC
1 CTTCCCCATCGGAAGGTGTTGTTTAG-TTTCCCAGTTTGCC
* * * *
103088 CTTCCTCACCGGAAGGTGTTGTCGAAGTCTACATTTCCCAGTTTTCC
1 CTTCCCCATCGGAAGGTGTTGT-----T-TA-GTTTCCCAGTTTGCC
* * * * * * *
103135 TTTCTCAATCGGAAGGTGTTGTTTAGTTTTCTAGCTTGCG
1 CTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCC
* ** * * *
103175 CTTCCCCACCCAAAAGTGTTGTCTACATTTCCCAGTTTGCC
1 CTTCCCCATCGGAAGGTGTTGTTTA-GTTTCCCAGTTTGCC
* * *
103216 TTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTA-TCTGCC
1 CTTCCCCATCGGAAGGTGTTGTTTAG-TTTCCCAGTTTGCC
* *
103256 CTTCCACA-CTGGAAGGGGTTGTTT
1 CTTCCCCATC-GGAAGGTGTTGTTT
103280 GCTCTTCTTA
Statistics
Matches: 331, Mismatches: 85, Indels: 50
0.71 0.18 0.11
Matches are distributed among these distances:
36 24 0.07
37 3 0.01
38 1 0.00
39 2 0.01
40 86 0.26
41 132 0.40
42 14 0.04
43 2 0.01
44 3 0.01
45 3 0.01
46 4 0.01
47 33 0.10
48 24 0.07
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (40 bp):
CTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAGTTTGCC
Found at i:102980 original size:166 final size:169
Alignment explanation
Indices: 102736--103163 Score: 517
Period size: 166 Copynumber: 2.5 Consensus size: 169
102726 CTAGTTCTAC
* *
102736 TTTTCCGCAAATTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTTTCCCAAATTTCTC
1 TTTTCC-CAACTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTTTCCCAAATTTCCC
* * *
102801 TTCTCCATCGGAAGGTGTTCTTTAGTTTCCCAGTATG-C-GCCC-ATCGGAAGTTGTTGCTT-AG
65 TTCTCCATCGGAAGGTGTTGTTTAGTTTCCCAATATGCCTGCCCGATCGGAAGATGTTGCTTAAG
* *
102862 TTTTCCTGTTTTGCCCTTCCCCACCAAAAGGTGTTGTTTAAG
130 TTTCCCAG-TTTGCCCTTCCCCACCAAAAGGTGTTGTTT-AG
** * * *
102904 -TTTCCCAGTTTGCCCTTTCTCATCGGAAGGTGTCGTCTAAGTCTACTTTTTCCCAAATTGCCCT
1 TTTTCCCAACTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTTTCCCAAATTTCCCT
* * * * *
102968 TCCCCATCGGAAGGTGTTGTTTAGTTTCCCAATTTGCCCTTCCCGGTCGGAAGATGTTGTTTAAG
66 TCTCCATCGGAAGGTGTTGTTTAGTTTCCCAATATG-CCTGCCCGATCGGAAGATGTTGCTTAAG
****
103033 TTTCCCAGTTTGCCCTTCCCCATGGGAAGGTGTTGTTTAG
130 TTTCCCAGTTTGCCCTTCCCCACCAAAAGGTGTTGTTTAG
* * * * ** *
103073 TTTTTCCAACTTGCCCTTCCTCACCGGAAGGTGTTGTCGAAGTCTAC-ATTTCCCAGTTTTCCTT
1 TTTTCCCAACTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTTTCCCAAATTTCCCT
*
103137 TCTCAATCGGAAGGTGTTGTTTAGTTT
66 TCTCCATCGGAAGGTGTTGTTTAGTTT
103164 TCTAGCTTGC
Statistics
Matches: 220, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
166 85 0.39
167 5 0.02
168 1 0.00
169 42 0.19
170 79 0.36
171 8 0.04
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (169 bp):
TTTTCCCAACTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTTTCCCAAATTTCCCT
TCTCCATCGGAAGGTGTTGTTTAGTTTCCCAATATGCCTGCCCGATCGGAAGATGTTGCTTAAGT
TTCCCAGTTTGCCCTTCCCCACCAAAAGGTGTTGTTTAG
Found at i:103224 original size:169 final size:168
Alignment explanation
Indices: 102745--103277 Score: 474
Period size: 169 Copynumber: 3.2 Consensus size: 168
102735 CTTTTCCGCA
* * * * *
102745 AATTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTTTCCCAAATTTCTCTTCTCC-AT
1 AATTGCCCTTCCTCACCGGAAGGTGTTGTCGAAGTCTACTATTTCCCAAATTGCCCTTC-CCAAT
* * * * ** * * *
102809 CGGAAGGTGTTCTTTAGTTTCCC-AGTATG--C-GCCCA-TCGGAAGTTGTTG-CTTAGTTTTCC
65 CGGAAGGTGTTGTTTAGTTTCCCAACT-TGCCCTTCCCACCCAAAAGATGTTGTCTAAGTTTCCC
* * ** *
102868 TGTTTTGCCCTTCCCCACCAAAAGGTGTTGTTTAAGTTTCCC
129 AG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AGTTTTCC
* * * * * * *
102910 AGTTTGCCCTTTCTCATCGGAAGGTGTCGTCTAAGTCTACTTTTTCCCAAATTGCCCTTCCCCAT
1 A-ATTGCCCTTCCTCACCGGAAGGTGTTGTCGAAGTCTACTATTTCCCAAATTGCCCTTCCCAAT
* *** ** *
102975 CGGAAGGTGTTGTTTAGTTTCCCAATTTGCCCTTCCCGGTCGGAAGATGTTGTTTAAGTTTCCCA
65 CGGAAGGTGTTGTTTAGTTTCCCAACTTGCCCTTCCCACCCAAAAGATGTTGTCTAAGTTTCCCA
*
103040 GTTTGCCCTTCCCCATGGGAAGGTGTTGTTTAGTTTTTCC
130 GTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG-TTTTCC
** * * *
103080 AACTTGCCCTTCCTCACCGGAAGGTGTTGTCGAAGTCTAC-ATTTCCCAGTTTTCCTTTCTCAAT
1 AA-TTGCCCTTCCTCACCGGAAGGTGTTGTCGAAGTCTACTATTTCCCAAATTGCCCTTCCCAAT
* * * *
103144 CGGAAGGTGTTGTTTAGTTTTCTAGCTTGCGCTTCCCCACCCAAAAG-TGTTGTCTACA-TTTCC
65 CGGAAGGTGTTGTTTAGTTTCCCAACTTGCCCTT-CCCACCCAAAAGATGTTGTCTA-AGTTTCC
*
103207 CAGTTTGCCTTTCCCCATCGGAAGGTGTTGTTTAGTTTTCC
128 CAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCC
* * * *
103248 TATCTGCCCTTCCACACTGGAAGGGGTTGT
1 AAT-TGCCCTTCCTCACCGGAAGGTGTTGT
103278 TTGCTCTTCT
Statistics
Matches: 307, Mismatches: 48, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
165 3 0.01
166 79 0.26
167 3 0.01
168 31 0.10
169 97 0.32
170 85 0.28
171 9 0.03
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (168 bp):
AATTGCCCTTCCTCACCGGAAGGTGTTGTCGAAGTCTACTATTTCCCAAATTGCCCTTCCCAATC
GGAAGGTGTTGTTTAGTTTCCCAACTTGCCCTTCCCACCCAAAAGATGTTGTCTAAGTTTCCCAG
TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCC
Found at i:103277 original size:81 final size:81
Alignment explanation
Indices: 102952--103277 Score: 293
Period size: 81 Copynumber: 3.9 Consensus size: 81
102942 AAGTCTACTT
** * * **
102952 TTTCCCAAATTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCCCAAT-TTGCCCTTCCCGGTC
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTATCTTGCCCTTCCC-ACC
** *
103016 GGAAGATGTTGTTTA-A
65 GGAAGGGGTTGTCTACA
* *
103032 GTTTCCCAGTTTGCCCTTCCCCATGGGAAGGTGTTGTTTAGTTTTTCC-AACTTGCCCTTCCTCA
1 -TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG-TTTTCCTATCTTGCCCTTCC-CA
*
103096 CCGGAAGGTGTTGTCGAAGTCTACA
63 CCGGAAGG-G--GT---TGTCTACA
* * * * * *
103121 TTTCCCAGTTTTCCTTTCTCAATCGGAAGGTGTTGTTTAGTTTT-CTAGCTTGCGCTTCCCCACC
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTATCTTGCCCTT-CCCACC
** * *
103185 CAAAAGTGTTGTCTACA
65 GGAAGGGGTTGTCTACA
* *
103202 TTTCCCAGTTTGCCTTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTATC-TGCCCTTCCACACT
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTATCTTGCCCTTCC-CACC
103266 GGAAGGGGTTGT
65 GGAAGGGGTTGT
103278 TTGCTCTTCT
Statistics
Matches: 198, Mismatches: 33, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
80 2 0.01
81 103 0.52
82 25 0.13
83 1 0.01
84 2 0.01
85 2 0.01
86 1 0.01
87 20 0.10
88 41 0.21
89 1 0.01
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (81 bp):
TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTATCTTGCCCTTCCCACCG
GAAGGGGTTGTCTACA
Found at i:103348 original size:50 final size:50
Alignment explanation
Indices: 103292--103726 Score: 504
Period size: 50 Copynumber: 8.8 Consensus size: 50
103282 TCTTCTTATT
* *
103292 CCAAAATGCCCATTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
* * * *
103342 ACAAAATGCCCCTTCCCGGTCGAAAGGTCACTGTTTCCTTTATCTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
*
103392 CCAAAAAT-CCCCTTCCCGGTCGAAAGGTCACTGTTTTCTTT-TTGTGTTT-
1 CC-AAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATT-TGTTTC
* * * * **
103441 CCAAAATGCCCCTTCCCGGTCGGAAGTTCCCTATTTTCTTTATCTACTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
* * * *
103491 CCAAAATGCCCCTTCGCGGTCGGAAGGTCCCTATTTTCTATATTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
* * * * * *
103541 CCAAAATGCCCATTCCCGATCAGAAGGTCCCTATTTCCTTTATTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
* * * *
103591 CTAAAATGCCCCTTCCTGGTCGGAAGGTCGCTGTTCTCTTTATTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
** * * * *
103641 CCAAAATGCCATTTCCTGGTTGGAAGGTC-CAGTTTTCTTTCTTTG-TTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
*
103689 CCAAAATGCCCCTTCCCGGTCGGAAGGTC-CAGTTTTCT
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCT
103727 CTTCACATTT
Statistics
Matches: 334, Mismatches: 46, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
48 42 0.13
49 48 0.14
50 239 0.72
51 5 0.01
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.36
Consensus pattern (50 bp):
CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTTTC
Found at i:103568 original size:149 final size:146
Alignment explanation
Indices: 103290--103726 Score: 497
Period size: 149 Copynumber: 2.9 Consensus size: 146
103280 GCTCTTCTTA
* *
103290 TTCCAAAATGCCCATTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCACAAAATGCCCCT
1 TTCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAATGCCCCT
* * * * *
103355 TCCCGGTCGAAAGGTCACTGTTTCCTTTATCTGTTTCCCAAAAAT-CCCCTTCCCGGTCGAAAGG
66 T-CCGGTCGGAAGGTCCCTATTTTCTTTATTTGTTTCCC-AAAATGCCCCTTCCCGGTCG-AAGG
103419 TCACTGTTTTCTTT-TTGTGT
128 TC-CTGTTTTCTTTATT-TGT
* * * **
103439 TTCCAAAATGCCCCTTCCCGGTCGGAAGTTCCCTATTTTCTTTATCTACTTCCCAAAATGCCCCT
1 TTCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAATGCCCCT
* * *
103504 TCGCGGTCGGAAGGTCCCTATTTTCTATATTTGTTTCCCAAAATGCCCATTCCCGATCAGAAGGT
66 TC-CGGTCGGAAGGTCCCTATTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTC-GAAGGT
* *
103569 CCCTATTTCCTTTATTTGT
129 -CCTGTTTTCTTTATTTGT
* * * * **
103588 TTCCTAAAATGCCCCTTCCTGGTCGGAAGGTCGCTGTTCTCTTTATTTGTTTCCCAAAATGCCAT
1 TTCC-AAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAATGCCCC
* *
103653 TTCCTGGTTGGAAGGT-CC-AGTTTTCTTTCTTTG-TTCCCAAAATGCCCCTTCCCGGTCGGAAG
65 TTCC-GGTCGGAAGGTCCCTA-TTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTC-GAAG
*
103715 GTCCAGTTTTCT
127 GTCCTGTTTTCT
103727 CTTCACATTT
Statistics
Matches: 244, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
147 7 0.03
148 35 0.14
149 135 0.55
150 67 0.27
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.37
Consensus pattern (146 bp):
TTCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATCTGTTTCCCAAAATGCCCCT
TCCGGTCGGAAGGTCCCTATTTTCTTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGAAGGTCC
TGTTTTCTTTATTTGT
Found at i:104617 original size:18 final size:17
Alignment explanation
Indices: 104590--104625 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
104580 TTTCTTTTCA
*
104590 TCTATTTTTCTTTTAGT
1 TCTATTTTTCTTCTAGT
104607 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
104625 T
1 T
104626 TTAGGTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.11, C:0.14, G:0.08, T:0.67
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:106525 original size:18 final size:18
Alignment explanation
Indices: 106502--106537 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
106492 GTCTAATCAG
106502 TCCCCTATAAATAGCCAC
1 TCCCCTATAAATAGCCAC
106520 TCCCCTATAAATAGCCAC
1 TCCCCTATAAATAGCCAC
106538 CTTATGTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.39, G:0.06, T:0.22
Consensus pattern (18 bp):
TCCCCTATAAATAGCCAC
Found at i:107939 original size:65 final size:65
Alignment explanation
Indices: 107857--107980 Score: 230
Period size: 65 Copynumber: 1.9 Consensus size: 65
107847 AACGCATAAG
107857 CCTAGCTTTTGCTTCTTTATTCGACATCAAGTAGCGGAGTGCAGCATGATCGGAATAGATTATTA
1 CCTAGCTTTTGCTTCTTTATTCGACATCAAGTAGCGGAGTGCAGCATGATCGGAATAGATTATTA
* *
107922 CCTAGCTTTTTCTTCTTTATTCGACATCAAGTAGCTGAGTGCAGCATGATCGGAATAGA
1 CCTAGCTTTTGCTTCTTTATTCGACATCAAGTAGCGGAGTGCAGCATGATCGGAATAGA
107981 CATCGAGATG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (65 bp):
CCTAGCTTTTGCTTCTTTATTCGACATCAAGTAGCGGAGTGCAGCATGATCGGAATAGATTATTA
Found at i:113900 original size:12 final size:12
Alignment explanation
Indices: 113885--113909 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
113875 GACAAAAGGA
113885 AAATCAAAACTT
1 AAATCAAAACTT
113897 AAATCAAAACTT
1 AAATCAAAACTT
113909 A
1 A
113910 CCATCTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATCAAAACTT
Found at i:117576 original size:21 final size:21
Alignment explanation
Indices: 117552--117609 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
117542 ATAAAGTTAT
*
117552 TAAAAAGCTTAATAAGAGTT-C
1 TAAAAATCTTAATAAGA-TTAC
* **
117573 TAAAATTCACAATAAGATTAC
1 TAAAAATCTTAATAAGATTAC
117594 TAAAAATCTTAATAAG
1 TAAAAATCTTAATAAG
117610 GTTAGGTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (21 bp):
TAAAAATCTTAATAAGATTAC
Found at i:120490 original size:32 final size:32
Alignment explanation
Indices: 120444--120534 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 32
120434 TTTGGTCAAA
* *
120444 ACCCAAACTGAACCCGAACCTGAATTAACC-T
1 ACCCAAATTCAACCCGAACCTGAATTAACCAT
* *
120475 GACCCAAATTCAACCCAAACCCGAATTAACCAT
1 -ACCCAAATTCAACCCGAACCTGAATTAACCAT
* *
120508 ACCAAAATTCAACCCG-ACCTGACTTAA
1 ACCCAAATTCAACCCGAACCTGAATTAA
120535 GCCCGAACCC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 9 0.18
32 40 0.80
33 1 0.02
ACGTcount: A:0.41, C:0.35, G:0.08, T:0.16
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAACCTGAATTAACCAT
Found at i:121653 original size:21 final size:21
Alignment explanation
Indices: 121629--121669 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
121619 TAACTCTAAA
121629 CACAACTTACACAACCTCAAC
1 CACAACTTACACAACCTCAAC
*
121650 CACAATTTACACAACCTCAA
1 CACAACTTACACAACCTCAA
121670 ACACTTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.39, G:0.00, T:0.17
Consensus pattern (21 bp):
CACAACTTACACAACCTCAAC
Found at i:127462 original size:2 final size:2
Alignment explanation
Indices: 127455--127491 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
127445 CGACCGATTA
*
127455 AT AT AT AT AT AT AT AT AT -T AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Done.